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Pérez-Roldán J, Henn L, Bernués J, Torras-LLort M, Tamirisa S, Belloc E, Rodríguez-Muñoz L, Timinszky G, Jiménez G, Méndez R, Carbonell A, Azorín F. Maternal histone mRNAs are uniquely processed through polyadenylation in a Stem-Loop Binding Protein (SLBP) dependent manner. Nucleic Acids Res 2025; 53:gkaf288. [PMID: 40239992 PMCID: PMC11997800 DOI: 10.1093/nar/gkaf288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 03/22/2025] [Accepted: 04/01/2025] [Indexed: 04/18/2025] Open
Abstract
During early embryogenesis the zygotic genome remains transcriptionally silent and expression relies on maternally deposited products. Maternal deposition of histones is crucial to preserve chromatin integrity during early embryo development, when the number of nuclei exponentially increases in the absence of zygotic expression. In the Drosophila embryo, histones are maternally deposited as both proteins and mRNAs. Histone transcripts are the only nonpolyadenylated cellular mRNAs. They contain a highly conserved 3'UTR stem-loop structure, which is recognized by the Stem-Loop Binding Protein (SLBP) that, in conjunction with U7 snRNP, regulates their unique 3'-end processing. Here we report that, unexpectedly, maternal histone mRNAs are polyadenylated and have a truncated 3' stem-loop. This noncanonical 3'-end processing of maternal histone mRNAs occurs at their synthesis during oogenesis and requires SLBP, but not U7 snRNP. We show that maternal histone transcripts are subjected to cytoplasmic poly(A) tail elongation by Wisp, which results in their stabilization and is a requisite for translation. We also show that maternal histone transcripts remain largely quiescent and that their translation is activated upon loss of the embryonic linker histone dBigH1, which impairs chromatin assembly and induces DNA damage. Here, we discuss possible models to integrate these observations.
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Affiliation(s)
- Juan Pérez-Roldán
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona. Spain
| | - László Henn
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
| | - Jordi Bernués
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona. Spain
| | - Mònica Torras-LLort
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona. Spain
| | - Srividya Tamirisa
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona. Spain
| | - Eulàlia Belloc
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona. Spain
| | - Laura Rodríguez-Muñoz
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain
| | - Gyula Timinszky
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
| | - Gerardo Jiménez
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Raúl Méndez
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona. Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Albert Carbonell
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona. Spain
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona. Spain
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2
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Mi Y, Yan L, Wu Y, Zheng Y. Deficiency of UBE3D in mice leads to severe embryonic abnormalities and disrupts the mRNA of Homeobox genes via CPSF3. Cell Death Discov 2025; 11:99. [PMID: 40075082 PMCID: PMC11904178 DOI: 10.1038/s41420-025-02387-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 02/18/2025] [Accepted: 03/05/2025] [Indexed: 03/14/2025] Open
Abstract
Neurulation is a crucial event during vertebrate early embryogenesis, and abnormalities in this process can result in embryonic lethality or congenital disorders, such as neural tube defects. Through our previous phenotypic-driven screening in mice, we have identified UBE3D as a key factor for the neurulation process. By generating Ube3d knockout mice using CRISPR/Cas9 technology, we observed that homozygous mice exhibited severe growth retardation and malformation, ultimately dying between E10.5 to E11.5. In contrast to their wild-type and heterozygote littermates, homozygous embryos displayed small heads and unturned caudal neural tubes at E9.5. Our in situ hybridization and immunofluorescence experiments revealed high expression of UBE3D in the forebrain, neural tube, and heart at E9.5-10.5. Furthermore, RNA-seq analysis of the E10.5 embryos demonstrated that deficiency in UBE3D resulted in the downregulation of multiple Homeobox genes, including those specifically expressed in the forebrain and lumbosacral regions. We also discovered that UBE3D interacts with CPSF3, which is an endonuclease essential for the pre-mRNA 3' end process. UBE3D could de-ubiquitinate CPSF3, and a deficiency of UBE3D leads to reduced levels of CPSF3 in both mouse and human cells. Overexpression of dominant negative mutants of CPSF3 was found to partially reduce mRNA levels of several Homeobox genes. In summary, our findings highlight that UBE3D is critical for early embryonic development in mice.
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Affiliation(s)
- Yiwei Mi
- Institute of Developmental Biology & Molecular Medicine, Dept. of Cellular & Developmental Biology, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, 200433, China
- Obstetrics and Gynecology Hospital, The institute of Obstetrics and Gynecology, Fudan University, Shanghai, 200011, China
| | - Lu Yan
- Obstetrics and Gynecology Hospital, The institute of Obstetrics and Gynecology, Fudan University, Shanghai, 200011, China
| | - Yu Wu
- Institute of Developmental Biology & Molecular Medicine, Dept. of Cellular & Developmental Biology, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yufang Zheng
- Obstetrics and Gynecology Hospital, The institute of Obstetrics and Gynecology, Fudan University, Shanghai, 200011, China.
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3
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Zhang Y, Huang Z, Lu W, Liu Z. Alternative polyadenylation in cancer: Molecular mechanisms and clinical application. Crit Rev Oncol Hematol 2025; 206:104599. [PMID: 39701503 DOI: 10.1016/j.critrevonc.2024.104599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Accepted: 12/13/2024] [Indexed: 12/21/2024] Open
Abstract
Alternative polyadenylation (APA) serves as a crucial mechanism for the posttranscriptional regulation of gene expression and influences gene expression by generating diverse mRNA isoforms. This process is regulated by a diverse array of RNA-binding proteins (RBPs), which selectively bind to specific sequences or structures within the pre-mRNA molecule. Dysregulation of APA and its associated RBPs has been implicated in numerous diseases, including cardiovascular diseases, nervous system disease, and cancer. For instance, aberrant APA events have been observed in several types of tumors, contributing to tumor heterogeneity and affecting key cellular pathways involved in cell proliferation, invasion, metastasis, and response to therapy. This review critically evaluates the current understanding of APA mechanisms and the multifaceted roles of RBPs in orchestrating this intricate process. We highlight recent advancements in high-throughput sequencing and bioinformatics tools that have enhanced our ability to study APA on a genome-wide scale. Moreover, we explored the pathological consequences of APA dysregulation, emphasizing its role in oncogenesis. By elucidating the intricate relationships between APA and RBPs, this review aims to underscore the potential of targeting the APA machinery and RBPs for therapeutic intervention. Understanding these molecular processes holds promise for developing novel diagnostic markers and treatment strategies for a range of human cancers.
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Affiliation(s)
- Ying Zhang
- Department of Radiotherapy, Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, Guangdong 515041, China; Clinical Research Center, Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, Guangdong 515041, China.
| | - Zikun Huang
- Department of Orthopedics, First Affiliated Hospital of Shantou University Medical College, No.57 Changping Road, Shantou, Guangdong 515041, China
| | - Weiqing Lu
- Department of Radiotherapy, Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, Guangdong 515041, China
| | - Zhaoyong Liu
- Department of Orthopedics, First Affiliated Hospital of Shantou University Medical College, No.57 Changping Road, Shantou, Guangdong 515041, China.
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4
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Lopez Martinez D, Svejstrup JQ. Mechanisms of RNA Polymerase II Termination at the 3'-End of Genes. J Mol Biol 2025; 437:168735. [PMID: 39098594 DOI: 10.1016/j.jmb.2024.168735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/23/2024] [Accepted: 07/30/2024] [Indexed: 08/06/2024]
Abstract
RNA polymerase II (RNAPII) is responsible for the synthesis of a diverse set of RNA molecules, including protein-coding messenger RNAs (mRNAs) and many short non-coding RNAs (ncRNAs). For this purpose, RNAPII relies on a multitude of factors that regulate the transcription cycle, from initiation and promoter-proximal pausing, through elongation and finally termination. RNAPII transcription termination at the end of genes ensures the release of RNAPII from the DNA template and its efficient recycling for further rounds of transcription. Termination of RNAPII is tightly coupled to 3'-end mRNA processing, which constitutes an important trigger for the subsequent transcription termination event. In this review, we discuss the current understanding of RNAPII termination mechanisms, focusing on 'canonical' termination at the 3'-end of genes. We also integrate the allosteric and 'torpedo' models into a unified model of termination, and describe the different termination factors that have been identified to date, paying special attention to the human factors and their mechanism of action at the molecular level. Indeed, in recent years the development of novel approaches in structural biology, biochemistry and cell biology have together led to a more detailed comprehension of the different mechanisms of RNAPII termination, and a better understanding of their importance in regulating gene expression, especially under cellular stress and pathological situations.
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Affiliation(s)
- David Lopez Martinez
- Centre for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
| | - Jesper Q Svejstrup
- Centre for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
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5
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Sajek MP, Bilodeau DY, Beer MA, Horton E, Miyamoto Y, Velle KB, Eckmann L, Fritz-Laylin L, Rissland OS, Mukherjee N. Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists. Genome Res 2024; 34:1570-1581. [PMID: 39327029 PMCID: PMC11529991 DOI: 10.1101/gr.279526.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 09/11/2024] [Indexed: 09/28/2024]
Abstract
The poly(A) signal, together with auxiliary elements, directs cleavage of a pre-mRNA and thus determines the 3' end of the mature transcript. In many species, including humans, the poly(A) signal is an AAUAAA hexamer, but we recently found that the deeply branching eukaryote Giardia lamblia uses a distinct hexamer (AGURAA) and lacks any known auxiliary elements. Our discovery prompted us to explore the evolutionary dynamics of poly(A) signals and auxiliary elements in the eukaryotic kingdom. We use direct RNA sequencing to determine poly(A) signals for four protists within the Metamonada clade (which also contains G. lamblia) and two outgroup protists. These experiments reveal that the AAUAAA hexamer serves as the poly(A) signal in at least four different eukaryotic clades, indicating that it is likely the ancestral signal, whereas the unusual Giardia version is derived. We find that the use and relative strengths of auxiliary elements are also plastic; in fact, within Metamonada, species like G. lamblia make use of a previously unrecognized auxiliary element where nucleotides flanking the poly(A) signal itself specify genuine cleavage sites. Thus, despite the fundamental nature of pre-mRNA cleavage for the expression of all protein-coding genes, the motifs controlling this process are dynamic on evolutionary timescales, providing motivation for future biochemical and structural studies as well as new therapeutic angles to target eukaryotic pathogens.
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Affiliation(s)
- Marcin P Sajek
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
| | - Danielle Y Bilodeau
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Michael A Beer
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Emma Horton
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Yukiko Miyamoto
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Katrina B Velle
- Department of Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Lars Eckmann
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Lillian Fritz-Laylin
- Department of Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Olivia S Rissland
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA;
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Neelanjan Mukherjee
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA;
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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6
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Zoltner M, Horn D, Field MC. Pass the boron: benzoxaboroles as antiparasite drugs. Trends Parasitol 2024; 40:820-828. [PMID: 39107181 DOI: 10.1016/j.pt.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/11/2024] [Accepted: 07/11/2024] [Indexed: 08/09/2024]
Abstract
The development of new drug modalities has been facilitated recently by the introduction of boron as a component of organic compounds, and specifically within a benzoxaborale scaffold. This has enabled exploration of new chemical space and the development of effective compounds targeting a broad range of morbidities, including infections by protozoa, fungi, worms, and bacteria. Most notable is the recent demonstration of a single oral dose cure using acoziborole against African trypanosomiasis. Common and species-/structure-specific interactions between benzoxaboroles and parasite species have emerged and provide vital insights into the mechanisms of cidality, as well as potential challenges in terms of resistance and/or side effects. Here, we discuss the literature specific to benzoxaborole studies in parasitic protists and consider unanswered questions concerning this important new drug class.
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Affiliation(s)
- Martin Zoltner
- Department of Parasitology, Faculty of Science, Charles University in Prague, BIOCEV, Vestec, Czech Republic
| | - David Horn
- Biological Chemistry & Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Mark C Field
- Biological Chemistry & Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK; Institute of Parasitology, Faculty of Sciences, University of South Bohemia, 37005 České Budějovice, Czech Republic.
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7
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Liu L, Manley JL. Modulation of diverse biological processes by CPSF, the master regulator of mRNA 3' ends. RNA (NEW YORK, N.Y.) 2024; 30:1122-1140. [PMID: 38986572 PMCID: PMC11331416 DOI: 10.1261/rna.080108.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/27/2024] [Indexed: 07/12/2024]
Abstract
The cleavage and polyadenylation specificity factor (CPSF) complex plays a central role in the formation of mRNA 3' ends, being responsible for the recognition of the poly(A) signal sequence, the endonucleolytic cleavage step, and recruitment of poly(A) polymerase. CPSF has been extensively studied for over three decades, and its functions and those of its individual subunits are becoming increasingly well-defined, with much current research focusing on the impact of these proteins on the normal functioning or disease/stress states of cells. In this review, we provide an overview of the general functions of CPSF and its subunits, followed by a discussion of how they exert their functions in a surprisingly diverse variety of biological processes and cellular conditions. These include transcription termination, small RNA processing, and R-loop prevention/resolution, as well as more generally cancer, differentiation/development, and infection/immunity.
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Affiliation(s)
- Lizhi Liu
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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8
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Sun Q, Jin C. Cell signaling and epigenetic regulation of nicotine-induced carcinogenesis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 345:123426. [PMID: 38295934 PMCID: PMC10939829 DOI: 10.1016/j.envpol.2024.123426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/22/2023] [Accepted: 01/21/2024] [Indexed: 02/05/2024]
Abstract
Nicotine, a naturally occurring tobacco alkaloid responsible for tobacco addiction, has long been considered non-carcinogenic. However, emerging evidence suggests that nicotine may possess carcinogenic properties in mice and could be a potential carcinogen in humans. This review aims to summarize the potential molecular mechanisms underlying nicotine-induced carcinogenesis, with a specific focus on epigenetic regulation and the activation of nicotinic acetylcholine receptors (nAChRs) in addition to genotoxicity and excess reactive oxygen species (ROS). Additionally, we explore a novel hypothesis regarding nicotine's carcinogenicity involving the downregulation of stem-loop binding protein (SLBP), a critical regulator of canonical histone mRNA, and the polyadenylation of canonical histone mRNA. By shedding light on these mechanisms, this review underscores the need for further research to elucidate the carcinogenic potential of nicotine and its implications for human health.
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Affiliation(s)
- Qi Sun
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, 10010, USA; Department of Child and Adolescent Health, School of Public Health, China Medical University, Shenyang, Liaoning, 110013, China; Key Laboratory of Environmental Stress and Chronic Disease Control and Prevention, Ministry of Education, China Medical University, Shenyang, Liaoning, 110122, China
| | - Chunyuan Jin
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, 10010, USA; Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA.
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9
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Alahmari AA, Chaubey AH, Jonnakuti VS, Tisdale AA, Schwarz CD, Cornwell AC, Maraszek KE, Paterson EJ, Kim M, Venkat S, Gomez EC, Wang J, Gurova KV, Yalamanchili HK, Feigin ME. CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone mRNA processing. RNA (NEW YORK, N.Y.) 2024; 30:281-297. [PMID: 38191171 PMCID: PMC10870380 DOI: 10.1261/rna.079931.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 01/10/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited effective treatment options, potentiating the importance of uncovering novel drug targets. Here, we target cleavage and polyadenylation specificity factor 3 (CPSF3), the 3' endonuclease that catalyzes mRNA cleavage during polyadenylation and histone mRNA processing. We find that CPSF3 is highly expressed in PDAC and is associated with poor prognosis. CPSF3 knockdown blocks PDAC cell proliferation and colony formation in vitro and tumor growth in vivo. Chemical inhibition of CPSF3 by the small molecule JTE-607 also attenuates PDAC cell proliferation and colony formation, while it has no effect on cell proliferation of nontransformed immortalized control pancreatic cells. Mechanistically, JTE-607 induces transcriptional readthrough in replication-dependent histones, reduces core histone expression, destabilizes chromatin structure, and arrests cells in the S-phase of the cell cycle. Therefore, CPSF3 represents a potential therapeutic target for the treatment of PDAC.
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Affiliation(s)
- Abdulrahman A Alahmari
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Aditi H Chaubey
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Venkata S Jonnakuti
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Arwen A Tisdale
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Carla D Schwarz
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Abigail C Cornwell
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Kathryn E Maraszek
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Emily J Paterson
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Minsuh Kim
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Swati Venkat
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Eduardo Cortes Gomez
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Katerina V Gurova
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
| | - Hari Krishna Yalamanchili
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030, USA
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Michael E Feigin
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, USA
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10
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Russo M, Piccolo V, Polizzese D, Prosperini E, Borriero C, Polletti S, Bedin F, Marenda M, Michieletto D, Mandana GM, Rodighiero S, Cuomo A, Natoli G. Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription. Genes Dev 2023; 37:1017-1040. [PMID: 38092518 PMCID: PMC10760643 DOI: 10.1101/gad.351057.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023]
Abstract
Transcription termination pathways mitigate the detrimental consequences of unscheduled promiscuous initiation occurring at hundreds of thousands of genomic cis-regulatory elements. The Restrictor complex, composed of the Pol II-interacting protein WDR82 and the RNA-binding protein ZC3H4, suppresses processive transcription at thousands of extragenic sites in mammalian genomes. Restrictor-driven termination does not involve nascent RNA cleavage, and its interplay with other termination machineries is unclear. Here we show that efficient termination at Restrictor-controlled extragenic transcription units involves the recruitment of the protein phosphatase 1 (PP1) regulatory subunit PNUTS, a negative regulator of the SPT5 elongation factor, and Symplekin, a protein associated with RNA cleavage complexes but also involved in cleavage-independent and phosphatase-dependent termination of noncoding RNAs in yeast. PNUTS and Symplekin act synergistically with, but independently from, Restrictor to dampen processive extragenic transcription. Moreover, the presence of limiting nuclear levels of Symplekin imposes a competition for its recruitment among multiple transcription termination machineries, resulting in mutual regulatory interactions. Hence, by synergizing with Restrictor, Symplekin and PNUTS enable efficient termination of processive, long-range extragenic transcription.
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Affiliation(s)
- Marta Russo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Viviana Piccolo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Danilo Polizzese
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Elena Prosperini
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Carolina Borriero
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Sara Polletti
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Fabio Bedin
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Mattia Marenda
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Gaurav Madappa Mandana
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Simona Rodighiero
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy;
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11
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Fongang B, Wadop YN, Zhu Y, Wagner EJ, Kudlicki A, Rowicka M. Coevolution combined with molecular dynamics simulations provides structural and mechanistic insights into the interactions between the integrator complex subunits. Comput Struct Biotechnol J 2023; 21:5686-5697. [PMID: 38074468 PMCID: PMC10700540 DOI: 10.1016/j.csbj.2023.11.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 01/18/2024] Open
Abstract
Finding the 3D structure of large, multi-subunit complexes is difficult, despite recent advances in cryo-EM technology, due to remaining challenges to expressing and purifying subunits. Computational approaches that predict protein-protein interactions, including Direct Coupling Analysis (DCA), represent an attractive alternative for dissecting interactions within protein complexes. However, they are readily applicable only to small proteins due to high computational complexity and a high number of false positives. To solve this problem, we proposed a modified DCA approach, a powerful tool to predict the most likely interfaces of protein complexes. Since our modified approach cannot provide structural and mechanistic details of interacting peptides, we combine it with Molecular Dynamics (MD) simulations. To illustrate this novel approach, we predict interacting domains and structural details of interactions of two Integrator complex subunits, INTS9 and INTS11. Our predictions of interacting residues of INTS9/INTS11 are highly consistent with crystallographic structure. We then expand our procedure to two complexes whose structures are not well-studied: 1) The heterodimer formed by the Cleavage and Polyadenylation Specificity Factor 100-kD (CPSF100) and 73-kD (CPSF73); 2) The heterotrimer formed by INTS4/INTS9/INTS11. Experimental data supports our predictions of interactions within these two complexes, demonstrating that combining DCA and MD simulations is a powerful approach to revealing structural insights of large protein complexes.
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Affiliation(s)
- Bernard Fongang
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
- Department of Population Health Sciences, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
- Institute for Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United States
| | - Yannick N. Wadop
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
- Institute for Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United States
| | - Yingjie Zhu
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, United States
- Institute for Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United States
| | - Eric J. Wagner
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, United States
- Department of Biochemistry and Biophysics, The University of Rochester Medical Center, Rochester, NY, United States
- Institute for Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United States
| | - Andrzej Kudlicki
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, United States
- Institute for Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United States
- Informatics Service Center, The University of Texas Medical Branch, Galveston, TX, United States
| | - Maga Rowicka
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, United States
- Institute for Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United States
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12
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Thore S, Raoelijaona F, Talenton V, Fribourg S, Mackereth CD. Molecular details of the CPSF73-CPSF100 C-terminal heterodimer and interaction with Symplekin. Open Biol 2023; 13:230221. [PMID: 37989222 PMCID: PMC10688271 DOI: 10.1098/rsob.230221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/27/2023] [Indexed: 11/23/2023] Open
Abstract
Eukaryotic pre-mRNA is processed by a large multiprotein complex to accurately cleave the 3' end, and to catalyse the addition of the poly(A) tail. Within this cleavage and polyadenylation specificity factor (CPSF) machinery, the CPSF73/CPSF3 endonuclease subunit directly contacts both CPSF100/CPSF2 and the scaffold protein Symplekin to form a subcomplex known as the core cleavage complex or mammalian cleavage factor. Here we have taken advantage of a stable CPSF73-CPSF100 minimal heterodimer from Encephalitozoon cuniculi to determine the solution structure formed by the first and second C-terminal domain (CTD1 and CTD2) of both proteins. We find a large number of contacts between both proteins in the complex, and notably in the region between CTD1 and CTD2. A similarity is also observed between CTD2 and the TATA-box binding protein (TBP) domains. Separately, we have determined the structure of the terminal CTD3 domain of CPSF73, which also belongs to the TBP domain family and is connected by a flexible linker to the rest of CPSF73. Biochemical assays demonstrate a key role for the CTD3 of CPSF73 in binding Symplekin, and structural models of the trimeric complex from other species allow for comparative analysis and support an overall conserved architecture.
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Affiliation(s)
- Stéphane Thore
- Inserm, CNRS, ARNA Laboratory, Univ. Bordeaux, U1212, UMR 5320, 33000 Bordeaux, France
| | - Finaritra Raoelijaona
- Inserm, CNRS, ARNA Laboratory, Univ. Bordeaux, U1212, UMR 5320, 33000 Bordeaux, France
| | - Vincent Talenton
- Inserm, CNRS, ARNA Laboratory, Univ. Bordeaux, Institut Européen de Chimie et Biologie, U1212, UMR 5320, 33600 Pessac, France
| | - Sébastien Fribourg
- Inserm, CNRS, ARNA Laboratory, Univ. Bordeaux, U1212, UMR 5320, 33000 Bordeaux, France
| | - Cameron D. Mackereth
- Inserm, CNRS, ARNA Laboratory, Univ. Bordeaux, Institut Européen de Chimie et Biologie, U1212, UMR 5320, 33600 Pessac, France
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13
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Hao S, Zhang L, Zhao D, Zhou J, Ye C, Qu H, Li QQ. Inhibitor AN3661 reveals biological functions of Arabidopsis CLEAVAGE and POLYADENYLATION SPECIFICITY FACTOR 73. PLANT PHYSIOLOGY 2023; 193:537-554. [PMID: 37335917 DOI: 10.1093/plphys/kiad352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/09/2023] [Accepted: 05/21/2023] [Indexed: 06/21/2023]
Abstract
Cleavage and polyadenylation specificity factor (CPSF) is a protein complex that plays an essential biochemical role in mRNA 3'-end formation, including poly(A) signal recognition and cleavage at the poly(A) site. However, its biological functions at the organismal level are mostly unknown in multicellular eukaryotes. The study of plant CPSF73 has been hampered by the lethality of Arabidopsis (Arabidopsis thaliana) homozygous mutants of AtCPSF73-I and AtCPSF73-II. Here, we used poly(A) tag sequencing to investigate the roles of AtCPSF73-I and AtCPSF73-II in Arabidopsis treated with AN3661, an antimalarial drug with specificity for parasite CPSF73 that is homologous to plant CPSF73. Direct seed germination on an AN3661-containing medium was lethal; however, 7-d-old seedlings treated with AN3661 survived. AN3661 targeted AtCPSF73-I and AtCPSF73-II, inhibiting growth through coordinating gene expression and poly(A) site choice. Functional enrichment analysis revealed that the accumulation of ethylene and auxin jointly inhibited primary root growth. AN3661 affected poly(A) signal recognition, resulted in lower U-rich signal usage, caused transcriptional readthrough, and increased the distal poly(A) site usage. Many microRNA targets were found in the 3' untranslated region lengthened transcripts; these miRNAs may indirectly regulate the expression of these targets. Overall, this work demonstrates that AtCPSF73 plays important part in co-transcriptional regulation, affecting growth, and development in Arabidopsis.
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Affiliation(s)
- Saiqi Hao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Lidan Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Danhui Zhao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Jiawen Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Haidong Qu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA 91766, USA
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14
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Huang Y, Ji H, Dong J, Wang X, He Z, Cheng Z, Zhu Q. CPSF3 Promotes Pre-mRNA Splicing and Prevents CircRNA Cyclization in Hepatocellular Carcinoma. Cancers (Basel) 2023; 15:4057. [PMID: 37627085 PMCID: PMC10452738 DOI: 10.3390/cancers15164057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/03/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
CircRNAs are crucial in tumorigenesis and metastasis, and are comprehensively downregulated in hepatocellular carcinoma (HCC). Previous studies demonstrated that the back-splicing of circRNAs was closely related to 3'-end splicing. As a core executor of 3'-end cleavage, we hypothesized that CPSF3 modulated circRNA circularization. Clinical data were analyzed to establish the prognostic correlations. Cytological experiments were performed to determine the role of CPSF3 in HCC. A fluorescent reporter was employed to explore the back-splicing mechanism. The circRNAs regulated by CPSF3 were screened by RNA-seq and validated by PCR, and changes in downstream pathways were explored by molecular experiments. Finally, the safety and efficacy of the CPSF3 inhibitor JTE-607 were verified both in vitro and in vivo. The results showed that CPSF3 was highly expressed in HCC cells, promoting their proliferation and migration, and that a high CPSF3 level was predictive of a poor prognosis. A mechanistic study revealed that CPSF3 enhanced RNA cleavage, thereby reducing circRNAs, and increasing linear mRNAs. Furthermore, inhibition of CPSF3 by JET-607 suppressed the proliferation of HCC cells. Our findings indicate that the increase of CPSF3 in HCC promotes the shift of pre-mRNA from circRNA to linear mRNA, leading to uncontrolled cell proliferation. JTE-607 exerted a therapeutic effect on HCC by blocking CPSF3.
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Affiliation(s)
- Ying Huang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
| | - Haofei Ji
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
| | - Jiani Dong
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
| | - Xueying Wang
- China National Intellectual Property Administration, Beijing 100088, China;
| | - Zhilin He
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
| | - Zeneng Cheng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (Y.H.); (H.J.); (J.D.); (Z.H.); (Z.C.)
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15
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Abstract
Formation of the 3' end of a eukaryotic mRNA is a key step in the production of a mature transcript. This process is mediated by a number of protein factors that cleave the pre-mRNA, add a poly(A) tail, and regulate transcription by protein dephosphorylation. Cleavage and polyadenylation specificity factor (CPSF) in humans, or cleavage and polyadenylation factor (CPF) in yeast, coordinates these enzymatic activities with each other, with RNA recognition, and with transcription. The site of pre-mRNA cleavage can strongly influence the translation, stability, and localization of the mRNA. Hence, cleavage site selection is highly regulated. The length of the poly(A) tail is also controlled to ensure that every transcript has a similar tail when it is exported from the nucleus. In this review, we summarize new mechanistic insights into mRNA 3'-end processing obtained through structural studies and biochemical reconstitution and outline outstanding questions in the field.
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Affiliation(s)
- Vytautė Boreikaitė
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom;
| | - Lori A Passmore
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom;
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16
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Cao J, Kuyumcu-Martinez MN. Alternative polyadenylation regulation in cardiac development and cardiovascular disease. Cardiovasc Res 2023; 119:1324-1335. [PMID: 36657944 PMCID: PMC10262186 DOI: 10.1093/cvr/cvad014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/01/2022] [Accepted: 11/28/2022] [Indexed: 01/21/2023] Open
Abstract
Cleavage and polyadenylation of pre-mRNAs is a necessary step for gene expression and function. Majority of human genes exhibit multiple polyadenylation sites, which can be alternatively used to generate different mRNA isoforms from a single gene. Alternative polyadenylation (APA) of pre-mRNAs is important for the proteome and transcriptome landscape. APA is tightly regulated during development and contributes to tissue-specific gene regulation. Mis-regulation of APA is linked to a wide range of pathological conditions. APA-mediated gene regulation in the heart is emerging as a new area of research. Here, we will discuss the impact of APA on gene regulation during heart development and in cardiovascular diseases. First, we will briefly review how APA impacts gene regulation and discuss molecular mechanisms that control APA. Then, we will address APA regulation during heart development and its dysregulation in cardiovascular diseases. Finally, we will discuss pre-mRNA targeting strategies to correct aberrant APA patterns of essential genes for the treatment or prevention of cardiovascular diseases. The RNA field is blooming due to advancements in RNA-based technologies. RNA-based vaccines and therapies are becoming the new line of effective and safe approaches for the treatment and prevention of human diseases. Overall, this review will be influential for understanding gene regulation at the RNA level via APA in the heart and will help design RNA-based tools for the treatment of cardiovascular diseases in the future.
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Affiliation(s)
- Jun Cao
- Faculty of Environment and Life, Beijing University of Technology, Xueyuan Road, Haidian District, Beijing 100124, PR China
| | - Muge N Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77573, USA
- Department of Neurobiology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Translational Sciences, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77573, USA
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17
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Slight Variations in the Sequence Downstream of the Polyadenylation Signal Significantly Increase Transgene Expression in HEK293T and CHO Cells. Int J Mol Sci 2022; 23:ijms232415485. [PMID: 36555130 PMCID: PMC9779314 DOI: 10.3390/ijms232415485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
Compared to transcription initiation, much less is known about transcription termination. In particular, large-scale mutagenesis studies have, so far, primarily concentrated on promoter and enhancer, but not terminator sequences. Here, we used a massively parallel reporter assay (MPRA) to systematically analyze the influence of short (8 bp) sequence variants (mutations) located downstream of the polyadenylation signal (PAS) on the steady-state mRNA level of the upstream gene, employing an eGFP reporter and human HEK293T cells as a model system. In total, we evaluated 227,755 mutations located at different overlapping positions within +17..+56 bp downstream of the PAS for their ability to regulate the reporter gene expression. We found that the positions +17..+44 bp downstream of the PAS are more essential for gene upregulation than those located more distal to the PAS, and that the mutation sequences ensuring high levels of eGFP mRNA expression are extremely T-rich. Next, we validated the positive effect of a couple of mutations identified in the MPRA screening on the eGFP and luciferase protein expression. The most promising mutation increased the expression of the reporter proteins 13-fold and sevenfold on average in HEK293T and CHO cells, respectively. Overall, these findings might be useful for further improving the efficiency of production of therapeutic products, e.g., recombinant antibodies.
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18
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Liu J, Lu X, Zhang S, Yuan L, Sun Y. Molecular Insights into mRNA Polyadenylation and Deadenylation. Int J Mol Sci 2022; 23:ijms231910985. [PMID: 36232288 PMCID: PMC9570436 DOI: 10.3390/ijms231910985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/28/2022] Open
Abstract
Poly(A) tails are present on almost all eukaryotic mRNAs, and play critical roles in mRNA stability, nuclear export, and translation efficiency. The biosynthesis and shortening of a poly(A) tail are regulated by large multiprotein complexes. However, the molecular mechanisms of these protein machineries still remain unclear. Recent studies regarding the structural and biochemical characteristics of those protein complexes have shed light on the potential mechanisms of polyadenylation and deadenylation. This review summarizes the recent structural studies on pre-mRNA 3′-end processing complexes that initiate the polyadenylation and discusses the similarities and differences between yeast and human machineries. Specifically, we highlight recent biochemical efforts in the reconstitution of the active human canonical pre-mRNA 3′-end processing systems, as well as the roles of RBBP6/Mpe1 in activating the entire machinery. We also describe how poly(A) tails are removed by the PAN2-PAN3 and CCR4-NOT deadenylation complexes and discuss the emerging role of the cytoplasmic poly(A)-binding protein (PABPC) in promoting deadenylation. Together, these recent discoveries show that the dynamic features of these machineries play important roles in regulating polyadenylation and deadenylation.
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19
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Muckenfuss LM, Migenda Herranz AC, Boneberg FM, Clerici M, Jinek M. Fip1 is a multivalent interaction scaffold for processing factors in human mRNA 3' end biogenesis. eLife 2022; 11:80332. [PMID: 36073787 PMCID: PMC9512404 DOI: 10.7554/elife.80332] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022] Open
Abstract
3′ end formation of most eukaryotic mRNAs is dependent on the assembly of a ~1.5 MDa multiprotein complex, that catalyzes the coupled reaction of pre-mRNA cleavage and polyadenylation. In mammals, the cleavage and polyadenylation specificity factor (CPSF) constitutes the core of the 3′ end processing machinery onto which the remaining factors, including cleavage stimulation factor (CstF) and poly(A) polymerase (PAP), assemble. These interactions are mediated by Fip1, a CPSF subunit characterized by high degree of intrinsic disorder. Here, we report two crystal structures revealing the interactions of human Fip1 (hFip1) with CPSF30 and CstF77. We demonstrate that CPSF contains two copies of hFip1, each binding to the zinc finger (ZF) domains 4 and 5 of CPSF30. Using polyadenylation assays we show that the two hFip1 copies are functionally redundant in recruiting one copy of PAP, thereby increasing the processivity of RNA polyadenylation. We further show that the interaction between hFip1 and CstF77 is mediated via a short motif in the N-terminal ‘acidic’ region of hFip1. In turn, CstF77 competitively inhibits CPSF-dependent PAP recruitment and 3′ polyadenylation. Taken together, these results provide a structural basis for the multivalent scaffolding and regulatory functions of hFip1 in 3′ end processing.
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Affiliation(s)
| | | | | | - Marcello Clerici
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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20
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Sun Q, Chen D, Raja A, Grunig G, Zelikoff J, Jin C. Downregulation of Stem-Loop Binding Protein by Nicotine via α7-Nicotinic Acetylcholine Receptor and Its Role in Nicotine-Induced Cell Transformation. Toxicol Sci 2022; 189:186-202. [PMID: 35929799 PMCID: PMC9801712 DOI: 10.1093/toxsci/kfac080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The use of electronic-cigarettes (e-cigs) has increased substantially in recent years, particularly among the younger generations. Liquid nicotine is the main component of e-cigs. Previous studies have shown that mice exposed to e-cig aerosols developed lung adenocarcinoma and bladder hyperplasia. These findings implicated a potential role for e-cig aerosols and nicotine in cancer development, although the underlying mechanisms are not fully understood. Here we report that exposure to liquid nicotine or nicotine aerosol generated from e-cig induces downregulation of Stem-loop binding protein (SLBP) and polyadenylation of canonical histone mRNAs in human bronchial epithelial cells and in mice lungs. Canonical histone mRNAs typically do not end in a poly(A) tail and the acquisition of such a tail via depletion of SLBP has been shown to causes chromosome instability. We show that nicotine-induced SLBP depletion is reversed by an inhibitor of α7-nicotinic acetylcholine receptors (α7-nAChR) or siRNA specific for α7-nAChR, indicating a nAChR-dependent reduction of SLBP by nicotine. Moreover, PI3K/AKT pathway is activated by nicotine exposure and CK2 and probably CDK1, 2 kinases well known for their function for SLBP phosphorylation and degradation, are shown to be involved, α7-nAChR-dependently, in nicotine-induced SLBP depletion. Importantly, nicotine-induced anchorage-independent cell growth is attenuated by inhibition of α7-nAChR and is rescued by overexpression of SLBP. We propose that the SLBP depletion and polyadenylation of canonical histone mRNAs via activation of α7-nAChR and a series of downstream signal transduction pathways are critical for nicotine-induced cell transformation and potential carcinogenesis.
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Affiliation(s)
- Qi Sun
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, New York 10010, USA,Department of Child and Adolescent Health, School of Public Health, China Medical University, Shenyang, Liaoning 110013, China
| | - Danqi Chen
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, New York 10010, USA
| | - Amna Raja
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, New York 10010, USA
| | - Gabriele Grunig
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, New York 10010, USA,Department of Medicine, New York University Grossman School of Medicine, New York, New York 10010, USA
| | - Judith Zelikoff
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, New York 10010, USA
| | - Chunyuan Jin
- To whom correspondence should be addressed at Department of Environmental Medicine, New York University Grossman School of Medicine, 341E 25th Street, New York, NY 10010, USA. E-mail:
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21
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Bilodeau DY, Sheridan RM, Balan B, Jex AR, Rissland OS. Precise gene models using long-read sequencing reveal a unique poly(A) signal in Giardia lamblia. RNA (NEW YORK, N.Y.) 2022; 28:668-682. [PMID: 35110372 PMCID: PMC9014877 DOI: 10.1261/rna.078793.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
During pre-mRNA processing, the poly(A) signal is recognized by a protein complex that ensures precise cleavage and polyadenylation of the nascent transcript. The location of this cleavage event establishes the length and sequence of the 3' UTR of an mRNA, thus determining much of its post-transcriptional fate. Using long-read sequencing, we characterize the polyadenylation signal and related sequences surrounding Giardia lamblia cleavage sites for over 2600 genes. We find that G. lamblia uses an AGURAA poly(A) signal, which differs from the mammalian AAUAAA. We also describe how G. lamblia lacks common auxiliary elements found in other eukaryotes, along with the proteins that recognize them. Further, we identify 133 genes with evidence of alternative polyadenylation. These results suggest that despite pared-down cleavage and polyadenylation machinery, 3' end formation still appears to be an important regulatory step for gene expression in G. lamblia.
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Affiliation(s)
- Danielle Y Bilodeau
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Ryan M Sheridan
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Balu Balan
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC 3052, Australia
| | - Aaron R Jex
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC 3052, Australia
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Olivia S Rissland
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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22
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Spada S, Luke B, Danckwardt S. The Bidirectional Link Between RNA Cleavage and Polyadenylation and Genome Stability: Recent Insights From a Systematic Screen. Front Genet 2022; 13:854907. [PMID: 35571036 PMCID: PMC9095915 DOI: 10.3389/fgene.2022.854907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
The integrity of the genome is governed by multiple processes to ensure optimal survival and to prevent the inheritance of deleterious traits. While significant progress has been made to characterize components involved in the DNA Damage Response (DDR), little is known about the interplay between RNA processing and the maintenance of genome stability. Here, we describe the emerging picture of an intricate bidirectional coupling between RNA processing and genome integrity in an integrative manner. By employing insights from a recent large-scale RNAi screening involving the depletion of more than 170 components that direct (alternative) polyadenylation, we provide evidence of bidirectional crosstalk between co-transcriptional RNA 3′end processing and the DDR in a manner that optimizes genomic integrity. We provide instructive examples illustrating the wiring between the two processes and show how perturbations at one end are either compensated by buffering mechanisms at the other end, or even propel the initial insult and thereby become disease-eliciting as evidenced by various disorders.
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Affiliation(s)
- Stefano Spada
- Posttranscriptional Gene Regulation, University Medical Centre Mainz, Mainz, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, Germany
- Centre for Thrombosis and Hemostasis (CTH), University Medical Centre Mainz, Mainz, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg University, Mainz, Germany
| | - Sven Danckwardt
- Posttranscriptional Gene Regulation, University Medical Centre Mainz, Mainz, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, Germany
- Centre for Thrombosis and Hemostasis (CTH), University Medical Centre Mainz, Mainz, Germany
- German Centre for Cardiovascular Research (DZHK), Berlin, Germany
- Centre for Healthy Aging (CHA) Mainz, Mainz, Germany
- *Correspondence: Sven Danckwardt,
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23
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Wei L, Lai EC. Regulation of the Alternative Neural Transcriptome by ELAV/Hu RNA Binding Proteins. Front Genet 2022; 13:848626. [PMID: 35281806 PMCID: PMC8904962 DOI: 10.3389/fgene.2022.848626] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/01/2022] [Indexed: 11/30/2022] Open
Abstract
The process of alternative polyadenylation (APA) generates multiple 3' UTR isoforms for a given locus, which can alter regulatory capacity and on occasion change coding potential. APA was initially characterized for a few genes, but in the past decade, has been found to be the rule for metazoan genes. While numerous differences in APA profiles have been catalogued across genetic conditions, perturbations, and diseases, our knowledge of APA mechanisms and biology is far from complete. In this review, we highlight recent findings regarding the role of the conserved ELAV/Hu family of RNA binding proteins (RBPs) in generating the broad landscape of lengthened 3' UTRs that is characteristic of neurons. We relate this to their established roles in alternative splicing, and summarize ongoing directions that will further elucidate the molecular strategies for neural APA, the in vivo functions of ELAV/Hu RBPs, and the phenotypic consequences of these regulatory paradigms in neurons.
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Affiliation(s)
- Lu Wei
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Eric C. Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, United States
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24
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Schmidt M, Kluge F, Sandmeir F, Kühn U, Schäfer P, Tüting C, Ihling C, Conti E, Wahle E. Reconstitution of 3' end processing of mammalian pre-mRNA reveals a central role of RBBP6. Genes Dev 2022; 36:195-209. [PMID: 35177537 PMCID: PMC8887130 DOI: 10.1101/gad.349217.121] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/21/2022] [Indexed: 11/24/2022]
Abstract
The 3' ends of almost all eukaryotic mRNAs are generated in an essential two-step processing reaction: endonucleolytic cleavage of an extended precursor followed by the addition of a poly(A) tail. By reconstituting the reaction from overproduced and purified proteins, we provide a minimal list of 14 polypeptides that are essential and two that are stimulatory for RNA processing. In a reaction depending on the polyadenylation signal AAUAAA, the reconstituted system cleaves pre-mRNA at a single preferred site corresponding to the one used in vivo. Among the proteins, cleavage factor I stimulates cleavage but is not essential, consistent with its prominent role in alternative polyadenylation. RBBP6 is required, with structural data showing it to contact and presumably activate the endonuclease CPSF73 through its DWNN domain. The C-terminal domain of RNA polymerase II is dispensable. ATP, but not its hydrolysis, supports RNA cleavage by binding to the hClp1 subunit of cleavage factor II with submicromolar affinity.
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Affiliation(s)
- Moritz Schmidt
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Florian Kluge
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Felix Sandmeir
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Uwe Kühn
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Peter Schäfer
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Christian Tüting
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Christian Ihling
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
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25
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Kotian N, Troike KM, Curran KN, Lathia JD, McDonald JA. A Drosophila RNAi screen reveals conserved glioblastoma-related adhesion genes that regulate collective cell migration. G3 GENES|GENOMES|GENETICS 2022; 12:6388037. [PMID: 34849760 PMCID: PMC8728034 DOI: 10.1093/g3journal/jkab356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/06/2021] [Indexed: 11/14/2022]
Abstract
Abstract
Migrating cell collectives are key to embryonic development but also contribute to invasion and metastasis of a variety of cancers. Cell collectives can invade deep into tissues, leading to tumor progression and resistance to therapies. Collective cell invasion is also observed in the lethal brain tumor glioblastoma (GBM), which infiltrates the surrounding brain parenchyma leading to tumor growth and poor patient outcomes. Drosophila border cells, which migrate as a small cell cluster in the developing ovary, are a well-studied and genetically accessible model used to identify general mechanisms that control collective cell migration within native tissue environments. Most cell collectives remain cohesive through a variety of cell–cell adhesion proteins during their migration through tissues and organs. In this study, we first identified cell adhesion, cell matrix, cell junction, and associated regulatory genes that are expressed in human brain tumors. We performed RNAi knockdown of the Drosophila orthologs in border cells to evaluate if migration and/or cohesion of the cluster was impaired. From this screen, we identified eight adhesion-related genes that disrupted border cell collective migration upon RNAi knockdown. Bioinformatics analyses further demonstrated that subsets of the orthologous genes were elevated in the margin and invasive edge of human GBM patient tumors. These data together show that conserved cell adhesion and adhesion regulatory proteins with potential roles in tumor invasion also modulate collective cell migration. This dual screening approach for adhesion genes linked to GBM and border cell migration thus may reveal conserved mechanisms that drive collective tumor cell invasion.
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Affiliation(s)
- Nirupama Kotian
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Katie M Troike
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kristen N Curran
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Justin D Lathia
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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26
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Liu H, Moore CL. On the Cutting Edge: Regulation and Therapeutic Potential of the mRNA 3' End Nuclease. Trends Biochem Sci 2021; 46:772-784. [PMID: 33941430 PMCID: PMC8364479 DOI: 10.1016/j.tibs.2021.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/18/2021] [Accepted: 04/02/2021] [Indexed: 12/24/2022]
Abstract
Cleavage of nascent transcripts is a fundamental process for eukaryotic mRNA maturation and for the production of different mRNA isoforms. In eukaryotes, cleavage of mRNA precursors by the highly conserved endonuclease CPSF73 is critical for mRNA stability, export from the nucleus, and translation. As an essential enzyme in the cell, CPSF73 surprisingly shows promise as a drug target for specific cancers and for protozoan parasites. In this review, we cover our current understanding of CPSF73 in cleavage and polyadenylation, histone pre-mRNA processing, and transcription termination. We discuss the potential of CPSF73 as a target for novel therapeutics and highlight further research into the regulation of CPSF73 that will be critical to understanding its role in cancer and other diseases.
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Affiliation(s)
- Huiyun Liu
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Claire L Moore
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA.
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27
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Zhao R, Wang B, Guo Y, Zhang J, Chen D, He WM, Zhao YJ, Ding Y, Jin C, Li C, Zhao Y, Ren W, Fang L. Quantitative proteomics reveals arsenic attenuates stem-loop binding protein stability via a chaperone complex containing heat shock proteins and ERp44. Proteomics 2021; 21:e2100035. [PMID: 34132035 DOI: 10.1002/pmic.202100035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 12/25/2022]
Abstract
Arsenic pollution impacts health of millions of people in the world. Inorganic arsenic is a carcinogenic agent in skin and lung cancers. The stem-loop binding protein (SLBP) binds to the stem-loop of the canonical histone mRNA and regulates its metabolism during cell cycle. Our previous work has shown arsenic induces ubiquitin-proteasome dependent degradation of SLBP and contributes to lung cancer. In this study, we established the first comprehensive SLBP interaction network by affinity purification-mass spectrometry (AP-MS) analysis, and further demonstrated arsenic enhanced the association between SLBP and a crucial chaperone complex containing heat shock proteins (HSPs) and ERp44. Strikingly, knockdown of these proteins markedly rescued the protein level of SLBP under arsenic exposure conditions, and abolished the increasing migration capacity of BEAS-2B cells induced by arsenic. Taken together, our study provides a potential new mechanism that a chaperone complex containing HSPs and ERp44 attenuates the stability of SLBP under both normal and arsenic exposure conditions, which could be essential for arsenic-induced high cell migration.
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Affiliation(s)
- Ruoyu Zhao
- Jiangsu Key Laboratory of Molecular Medicine, Medical School & Chemistry and Biomedicine Innovation Center of Nanjing University, Nanjing, China.,The Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Binghao Wang
- Jiangsu Key Laboratory of Molecular Medicine, Medical School & Chemistry and Biomedicine Innovation Center of Nanjing University, Nanjing, China
| | - Yan Guo
- Jiangsu Key Laboratory of Molecular Medicine, Medical School & Chemistry and Biomedicine Innovation Center of Nanjing University, Nanjing, China
| | - Jingzi Zhang
- Jiangsu Key Laboratory of Molecular Medicine, Medical School & Chemistry and Biomedicine Innovation Center of Nanjing University, Nanjing, China
| | - Danqi Chen
- Department of Environmental Medicine & Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
| | - Wei Ming He
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yong Juan Zhao
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yibing Ding
- Jiangsu Key Laboratory of Molecular Medicine, Medical School & Chemistry and Biomedicine Innovation Center of Nanjing University, Nanjing, China
| | - Chunyuan Jin
- Department of Environmental Medicine & Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
| | - Chaojun Li
- Jiangsu Key Laboratory of Molecular Medicine, Medical School & Chemistry and Biomedicine Innovation Center of Nanjing University, Nanjing, China
| | - Yue Zhao
- Jiangsu Key Laboratory of Molecular Medicine, Medical School & Chemistry and Biomedicine Innovation Center of Nanjing University, Nanjing, China
| | - Wei Ren
- The Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Lei Fang
- Jiangsu Key Laboratory of Molecular Medicine, Medical School & Chemistry and Biomedicine Innovation Center of Nanjing University, Nanjing, China
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28
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Pfleiderer MM, Galej WP. Structure of the catalytic core of the Integrator complex. Mol Cell 2021; 81:1246-1259.e8. [PMID: 33548203 PMCID: PMC7980224 DOI: 10.1016/j.molcel.2021.01.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/29/2020] [Accepted: 01/05/2021] [Indexed: 12/17/2022]
Abstract
The Integrator is a specialized 3' end-processing complex involved in cleavage and transcription termination of a subset of nascent RNA polymerase II transcripts, including small nuclear RNAs (snRNAs). We provide evidence of the modular nature of the Integrator complex by biochemically characterizing its two subcomplexes, INTS5/8 and INTS10/13/14. Using cryoelectron microscopy (cryo-EM), we determined a 3.5-Å-resolution structure of the INTS4/9/11 ternary complex, which constitutes Integrator's catalytic core. Our structure reveals the spatial organization of the catalytic nuclease INTS11, bound to its catalytically impaired homolog INTS9 via several interdependent interfaces. INTS4, a helical repeat protein, plays a key role in stabilizing nuclease domains and other components. In this assembly, all three proteins form a composite electropositive groove, suggesting a putative RNA binding path within the complex. Comparison with other 3' end-processing machineries points to distinct features and a unique architecture of the Integrator's catalytic module.
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Affiliation(s)
- Moritz M Pfleiderer
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Wojciech P Galej
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France.
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29
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Chen D, Chen QY, Wang Z, Zhu Y, Kluz T, Tan W, Li J, Wu F, Fang L, Zhang X, He R, Shen S, Sun H, Zang C, Jin C, Costa M. Polyadenylation of Histone H3.1 mRNA Promotes Cell Transformation by Displacing H3.3 from Gene Regulatory Elements. iScience 2020; 23:101518. [PMID: 32920490 PMCID: PMC7492993 DOI: 10.1016/j.isci.2020.101518] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 07/17/2020] [Accepted: 08/26/2020] [Indexed: 12/17/2022] Open
Abstract
Replication-dependent canonical histone messenger RNAs (mRNAs) do not terminate with a poly(A) tail at the 3' end. We previously demonstrated that exposure to arsenic, an environmental carcinogen, induces polyadenylation of canonical histone H3.1 mRNA, causing transformation of human cells in vitro. Here we report that polyadenylation of H3.1 mRNA increases H3.1 protein, resulting in displacement of histone variant H3.3 at active promoters, enhancers, and insulator regions, leading to transcriptional deregulation, G2/M cell-cycle arrest, chromosome aneuploidy, and aberrations. In support of these observations, knocking down the expression of H3.3 induced cell transformation, whereas ectopic expression of H3.3 attenuated arsenic-induced cell transformation. Notably, arsenic exposure also resulted in displacement of H3.3 from active promoters, enhancers, and insulator regions. These data suggest that H3.3 displacement might be central to carcinogenesis caused by polyadenylation of H3.1 mRNA upon arsenic exposure. Our findings illustrate the importance of proper histone stoichiometry in maintaining genome integrity.
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Affiliation(s)
- Danqi Chen
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Qiao Yi Chen
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Zhenjia Wang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Yusha Zhu
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Thomas Kluz
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Wuwei Tan
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- Department of Statistics, University of Virginia, Charlottesville, VA 22904, USA
| | - Jinquan Li
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Feng Wu
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Lei Fang
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Xiaoru Zhang
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Rongquan He
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Steven Shen
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Hong Sun
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Chunyuan Jin
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Max Costa
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
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30
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Mendoza-Figueroa MS, Tatomer DC, Wilusz JE. The Integrator Complex in Transcription and Development. Trends Biochem Sci 2020; 45:923-934. [PMID: 32800671 DOI: 10.1016/j.tibs.2020.07.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/03/2020] [Accepted: 07/17/2020] [Indexed: 12/15/2022]
Abstract
The Integrator complex is conserved across metazoans and controls the fate of many nascent RNAs transcribed by RNA polymerase II (RNAPII). Among the 14 subunits of Integrator is an RNA endonuclease that is crucial for the biogenesis of small nuclear RNAs and enhancer RNAs. Integrator is further employed to trigger premature transcription termination at many protein-coding genes, thereby attenuating gene expression. Integrator thus helps to shape the transcriptome and ensure that genes can be robustly induced when needed. The molecular functions of Integrator subunits beyond the RNA endonuclease remain poorly understood, but some can act independently of the multisubunit complex. We highlight recent molecular insights into Integrator and propose how misregulation of this complex may lead to developmental defects and disease.
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Affiliation(s)
- María Saraí Mendoza-Figueroa
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Deirdre C Tatomer
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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31
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Hur W, Kemp JP, Tarzia M, Deneke VE, Marzluff WF, Duronio RJ, Di Talia S. CDK-Regulated Phase Separation Seeded by Histone Genes Ensures Precise Growth and Function of Histone Locus Bodies. Dev Cell 2020; 54:379-394.e6. [PMID: 32579968 DOI: 10.1016/j.devcel.2020.06.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 02/17/2020] [Accepted: 05/30/2020] [Indexed: 10/24/2022]
Abstract
Many membraneless organelles form through liquid-liquid phase separation, but how their size is controlled and whether size is linked to function remain poorly understood. The histone locus body (HLB) is an evolutionarily conserved nuclear body that regulates the transcription and processing of histone mRNAs. Here, we show that Drosophila HLBs form through phase separation. During embryogenesis, the size of HLBs is controlled in a precise and dynamic manner that is dependent on the cell cycle and zygotic histone gene activation. Control of HLB growth is achieved by a mechanism integrating nascent mRNAs at the histone locus, which facilitates phase separation, and the nuclear concentration of the scaffold protein multi-sex combs (Mxc), which is controlled by the activity of cyclin-dependent kinases. Reduced Cdk2 activity results in smaller HLBs and the appearance of nascent, misprocessed histone mRNAs. Thus, our experiments identify a mechanism linking nuclear body growth and size with gene expression.
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Affiliation(s)
- Woonyung Hur
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27705, USA
| | - James P Kemp
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marco Tarzia
- LPTMC, CNRS-UMR 7600, Sorbonne Université, 4 Pl. Jussieu, 75005 Paris, France
| | - Victoria E Deneke
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27705, USA
| | - William F Marzluff
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert J Duronio
- Department of Biology, Department of Genetics, Integrative Program for Biological and Genome Sciences, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stefano Di Talia
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27705, USA.
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32
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Gajdušková P, Ruiz de Los Mozos I, Rájecký M, Hluchý M, Ule J, Blazek D. CDK11 is required for transcription of replication-dependent histone genes. Nat Struct Mol Biol 2020; 27:500-510. [PMID: 32367068 PMCID: PMC7116321 DOI: 10.1038/s41594-020-0406-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 03/05/2020] [Indexed: 01/13/2023]
Abstract
Replication-dependent histones (RDH) are required for packaging of newly synthetized DNA into nucleosomes during S-phase when their expression is highly upregulated. However, the mechanisms of this upregulation in metazoan cells remain poorly understood. Using iCLIP and ChIP-seq, we found that human cyclin-dependent kinase 11 (CDK11) associates with RNA and chromatin of RDH genes primarily in the S-phase. Moreover, its N-terminal region binds FLASH, RDH-specific 3´end processing factor, which keeps the kinase on the chromatin. CDK11 phosphorylates serine 2 (Ser2) of the C-terminal domain (CTD) of RNA polymerase II (RNAPII), which is initiated at the middle of RDH genes and is required for further RNAPII elongation and 3´end processing. CDK11 depletion leads to decreased number of cells in S-phase, likely due to the function of CDK11 in RDH gene expression. Thus, the reliance of RDH expression on CDK11 could explain why CDK11 is essential for growth of many cancers.
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Affiliation(s)
- Pavla Gajdušková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Igor Ruiz de Los Mozos
- The Francis Crick Institute, London, UK.,Department of Neuromuscular Disease, Institute of Neurology, University College London, London, UK
| | - Michal Rájecký
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Milan Hluchý
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Jernej Ule
- The Francis Crick Institute, London, UK.,Department of Neuromuscular Disease, Institute of Neurology, University College London, London, UK
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.
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33
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Sun Y, Zhang Y, Aik WS, Yang XC, Marzluff WF, Walz T, Dominski Z, Tong L. Structure of an active human histone pre-mRNA 3'-end processing machinery. Science 2020; 367:700-703. [PMID: 32029631 DOI: 10.1126/science.aaz7758] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/31/2019] [Indexed: 01/10/2023]
Abstract
The 3'-end processing machinery for metazoan replication-dependent histone precursor messenger RNAs (pre-mRNAs) contains the U7 small nuclear ribonucleoprotein and shares the key cleavage module with the canonical cleavage and polyadenylation machinery. We reconstituted an active human histone pre-mRNA processing machinery using 13 recombinant proteins and two RNAs and determined its structure by cryo-electron microscopy. The overall structure is highly asymmetrical and resembles an amphora with one long handle. We captured the pre-mRNA in the active site of the endonuclease, the 73-kilodalton subunit of the cleavage and polyadenylation specificity factor, poised for cleavage. The endonuclease and the entire cleavage module undergo extensive rearrangements for activation, triggered through the recognition of the duplex between the authentic pre-mRNA and U7 small nuclear RNA (snRNA). Our study also has notable implications for understanding canonical and snRNA 3'-end processing.
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Affiliation(s)
- Yadong Sun
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Yixiao Zhang
- Laboratory of Molecular Electron Microscopy, Rockefeller University, New York, NY 10065, USA
| | - Wei Shen Aik
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Xiao-Cui Yang
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William F Marzluff
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, Rockefeller University, New York, NY 10065, USA.
| | - Zbigniew Dominski
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. .,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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34
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González-Mariscal L, Miranda J, Gallego-Gutiérrez H, Cano-Cortina M, Amaya E. Relationship between apical junction proteins, gene expression and cancer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183278. [PMID: 32240623 DOI: 10.1016/j.bbamem.2020.183278] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/09/2020] [Accepted: 03/06/2020] [Indexed: 12/11/2022]
Abstract
The apical junctional complex (AJC) is a cell-cell adhesion system present at the upper portion of the lateral membrane of epithelial cells integrated by the tight junction (TJ) and the adherens junction (AJ). This complex is crucial to initiate and stabilize cell-cell adhesion, to regulate the paracellular transit of ions and molecules and to maintain cell polarity. Moreover, we now consider the AJC as a hub of signal transduction that regulates cell-cell adhesion, gene transcription and cell proliferation and differentiation. The molecular components of the AJC are multiple and diverse and depending on the cellular context some of the proteins in this complex act as tumor suppressors or as promoters of cell transformation, migration and metastasis outgrowth. Here, we describe these new roles played by TJ and AJ proteins and their potential use in cancer diagnostics and as targets for therapeutic intervention.
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Affiliation(s)
- Lorenza González-Mariscal
- Department of Physiology, Biophysics and Neuroscience, Center of Research and Advanced Studies (Cinvestav), Mexico City, Mexico.
| | - Jael Miranda
- Department of Physiology, Biophysics and Neuroscience, Center of Research and Advanced Studies (Cinvestav), Mexico City, Mexico
| | - Helios Gallego-Gutiérrez
- Department of Physiology, Biophysics and Neuroscience, Center of Research and Advanced Studies (Cinvestav), Mexico City, Mexico
| | - Misael Cano-Cortina
- Department of Physiology, Biophysics and Neuroscience, Center of Research and Advanced Studies (Cinvestav), Mexico City, Mexico
| | - Elida Amaya
- Department of Physiology, Biophysics and Neuroscience, Center of Research and Advanced Studies (Cinvestav), Mexico City, Mexico
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35
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Murphy MR, Kleiman FE. Connections between 3' end processing and DNA damage response: Ten years later. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1571. [PMID: 31657151 PMCID: PMC7295566 DOI: 10.1002/wrna.1571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 12/23/2022]
Abstract
Ten years ago we reviewed how the cellular DNA damage response (DDR) is controlled by changes in the functional and structural properties of nuclear proteins, resulting in a timely coordinated control of gene expression that allows DNA repair. Expression of genes that play a role in DDR is regulated not only at transcriptional level during mRNA biosynthesis but also by changing steady-state levels due to turnover of the transcripts. The 3' end processing machinery, which is important in the regulation of mRNA stability, is involved in these gene-specific responses to DNA damage. Here, we review the latest mechanistic connections described between 3' end processing and DDR, with a special emphasis on alternative polyadenylation, microRNA and RNA binding proteins-mediated deadenylation, and discuss the implications of deregulation of these steps in DDR and human disease. This article is categorized under: RNA Processing > 3' End Processing RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Michael Robert Murphy
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
| | - Frida Esther Kleiman
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
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36
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Kurihara M, Komatsu K, Awane R, Inoue YH. Loss of Histone Locus Bodies in the Mature Hemocytes of Larval Lymph Gland Result in Hyperplasia of the Tissue in mxc Mutants of Drosophila. Int J Mol Sci 2020; 21:E1586. [PMID: 32111032 PMCID: PMC7084650 DOI: 10.3390/ijms21051586] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 02/15/2020] [Accepted: 02/24/2020] [Indexed: 01/22/2023] Open
Abstract
Mutations in the multi sex combs (mxc) gene in Drosophila results in malignant hyperplasia in larval hematopoietic tissues, called lymph glands (LG). mxc encodes a component of the histone locus body (HLB) that is essential for cell cycle-dependent transcription and processing of histone mRNAs. The mammalian nuclear protein ataxia-telangiectasia (NPAT) gene, encoded by the responsible gene for ataxia telangiectasia, is a functional Mxc orthologue. However, their roles in tumorigenesis are unclear. Genetic analyses of the mxc mutants and larvae having LG-specific depletion revealed that a reduced activity of the gene resulted in the hyperplasia, which is caused by hyper-proliferation of immature LG cells. The depletion of mxc in mature hemocytes of the LG resulted in the hyperplasia. Furthermore, the inhibition of HLB formation was required for LG hyperplasia. In the mutant larvae, the total mRNA levels of the five canonical histones decreased, and abnormal forms of polyadenylated histone mRNAs, detected rarely in normal larvae, were generated. The ectopic expression of the polyadenylated mRNAs was sufficient for the reproduction of the hyperplasia. The loss of HLB function, especially 3-end processing of histone mRNAs, is critical for malignant LG hyperplasia in this leukemia model in Drosophila. We propose that mxc is involved in the activation to induce adenosine deaminase-related growth factor A (Adgf-A), which suppresses immature cell proliferation in LG.
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Affiliation(s)
| | | | | | - Yoshihiro H. Inoue
- Department of Insect Biomedical Research, Center for Advanced Insect Research Promotion, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-0962, Japan; (M.K.); (K.K.); (R.A.)
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37
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Tatomer DC, Wilusz JE. Attenuation of Eukaryotic Protein-Coding Gene Expression via Premature Transcription Termination. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:83-93. [PMID: 32086332 DOI: 10.1101/sqb.2019.84.039644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A complex network of RNA transcripts is generated from eukaryotic genomes, many of which are processed in unexpected ways. Here, we highlight how premature transcription termination events at protein-coding gene loci can simultaneously lead to the generation of short RNAs and attenuate production of full-length mRNA transcripts. We recently showed that the Integrator (Int) complex can be selectively recruited to protein-coding gene loci, including Drosophila metallothionein A (MtnA), where the IntS11 RNA endonuclease cleaves nascent transcripts near their 5' ends. Such premature termination events catalyzed by Integrator can repress the expression of some full-length mRNAs by more than 100-fold. Transcription at small nuclear RNA (snRNA) loci is likewise terminated by Integrator cleavage, but protein-coding and snRNA gene loci have notably distinct dependencies on Integrator subunits. Additional mechanisms that attenuate eukaryotic gene outputs via premature termination have been discovered, including by the cleavage and polyadenylation machinery in a manner controlled by U1 snRNP. These mechanisms appear to function broadly across the transcriptome. This suggests that synthesis of full-length transcripts is not always the default option and that premature termination events can lead to a variety of transcripts, some of which may have important and unexpected biological functions.
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Affiliation(s)
- Deirdre C Tatomer
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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38
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Zhang Y, Sun Y, Shi Y, Walz T, Tong L. Structural Insights into the Human Pre-mRNA 3'-End Processing Machinery. Mol Cell 2020; 77:800-809.e6. [PMID: 31810758 PMCID: PMC7036032 DOI: 10.1016/j.molcel.2019.11.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/16/2019] [Accepted: 10/29/2019] [Indexed: 01/21/2023]
Abstract
The mammalian pre-mRNA 3'-end-processing machinery consists of cleavage and polyadenylation specificity factor (CPSF), cleavage stimulation factor (CstF), and other proteins, but the overall architecture of this machinery remains unclear. CPSF contains two functionally distinct modules: a cleavage factor (mCF) and a polyadenylation specificity factor (mPSF). Here, we have produced recombinant human CPSF and CstF and examined these factors by electron microscopy (EM). We find that mPSF is the organizational core of the machinery, while the conformations of mCF and CstF and the position of mCF relative to mPSF are highly variable. We have identified by cryo-EM a segment in CPSF100 that tethers mCF to mPSF, and we have named it the PSF interaction motif (PIM). Mutations in the PIM can abolish CPSF formation, indicating that it is a crucial contact in CPSF. We have also obtained reconstructions of mCF and CstF77 by cryo-EM, assembled around the mPSF core.
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Affiliation(s)
- Yixiao Zhang
- Laboratory of Molecular Electron Microscopy, Rockefeller University, New York, NY 10065, USA
| | - Yadong Sun
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Yongsheng Shi
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, Rockefeller University, New York, NY 10065, USA.
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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39
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Boskovic A, Bing XY, Kaymak E, Rando OJ. Control of noncoding RNA production and histone levels by a 5' tRNA fragment. Genes Dev 2019; 34:118-131. [PMID: 31831626 PMCID: PMC6938667 DOI: 10.1101/gad.332783.119] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/20/2019] [Indexed: 12/29/2022]
Abstract
In this study Boskovic et al. set out to elucidate the functions of a small RNA derived from the 5’ end of mature tRNA-Gly-GCC. Using several genomic, biochemical, and molecular methods, the authors reveal a conserved mechanism for 5’ tRNA fragment control of noncoding RNA biogenesis and global chromatin organization. Small RNAs derived from mature tRNAs, referred to as tRNA fragments or “tRFs,” are an emerging class of regulatory RNAs with poorly understood functions. We recently identified a role for one specific tRF—5′ tRF-Gly-GCC, or tRF-GG—as a repressor of genes associated with the endogenous retroelement MERVL, but the mechanistic basis for this regulation was unknown. Here, we show that tRF-GG plays a role in production of a wide variety of noncoding RNAs—snoRNAs, scaRNAs, and snRNAs—that are dependent on Cajal bodies for stability and activity. Among these noncoding RNAs, regulation of the U7 snRNA by tRF-GG modulates heterochromatin-mediated transcriptional repression of MERVL elements by supporting an adequate supply of histone proteins. Importantly, the effects of inhibiting tRF-GG on histone mRNA levels, on activity of a histone 3′ UTR reporter, and ultimately on MERVL regulation could all be suppressed by manipulating U7 RNA levels. We additionally show that the related RNA-binding proteins hnRNPF and hnRNPH bind directly to tRF-GG, and are required for Cajal body biogenesis, positioning these proteins as strong candidates for effectors of tRF-GG function in vivo. Together, our data reveal a conserved mechanism for 5′ tRNA fragment control of noncoding RNA biogenesis and, consequently, global chromatin organization.
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Affiliation(s)
- Ana Boskovic
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Xin Yang Bing
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Ebru Kaymak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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40
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Thore S, Fribourg S. Structural insights into the 3′-end mRNA maturation machinery: Snapshot on polyadenylation signal recognition. Biochimie 2019; 164:105-110. [DOI: 10.1016/j.biochi.2019.03.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/26/2019] [Indexed: 12/22/2022]
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41
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Kakegawa J, Sakane N, Suzuki K, Yoshida T. JTE-607, a multiple cytokine production inhibitor, targets CPSF3 and inhibits pre-mRNA processing. Biochem Biophys Res Commun 2019; 518:32-37. [PMID: 31399191 DOI: 10.1016/j.bbrc.2019.08.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 08/01/2019] [Indexed: 12/31/2022]
Abstract
JTE-607 is a small molecule that was developed as an inflammatory cytokine inhibitor and also as an anti-leukemia reagent for monocytic leukemia. However, the mode of action of JTE-607 remains unknown. In this study, we identified JTE-607 to be a prodrug compound that is converted to an active form by ester hydrolysis. Furthermore, we determined that the active form of JTE-607 bound cleavage and polyadenylation specificity factor subunit 3 (CPSF3), using compound-immobilized affinity chromatography. CPSF3 is a 73-kDa subunit of the cleavage and polyadenylation specificity factor complex, which functions as an RNA endonuclease. The protein is involved in the 3'-end processing of messenger RNA precursors (pre-mRNAs) at the cleavage site located downstream of the poly(A) addition signal. We found that treatment with JTE-607 caused accumulation of pre-mRNAs. Furthermore, knockdown experiments showed that CPSF3 deficiency also caused accumulation of pre-mRNAs and suppressed the expression of inflammatory cytokines, like JTE-607. These findings indicated that CPSF3 is a direct target of JTE-607 and a new potential target for the treatment of disease-related abnormal cytokine production.
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Affiliation(s)
- Junya Kakegawa
- Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa 236-0004, Japan
| | - Naoki Sakane
- Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa 236-0004, Japan
| | - Kensuke Suzuki
- Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa 236-0004, Japan
| | - Takayuki Yoshida
- Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa 236-0004, Japan.
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42
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Albrecht TR, Shevtsov SP, Wu Y, Mascibroda LG, Peart NJ, Huang KL, Sawyer IA, Tong L, Dundr M, Wagner EJ. Integrator subunit 4 is a 'Symplekin-like' scaffold that associates with INTS9/11 to form the Integrator cleavage module. Nucleic Acids Res 2019; 46:4241-4255. [PMID: 29471365 PMCID: PMC5934644 DOI: 10.1093/nar/gky100] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 02/17/2018] [Indexed: 12/14/2022] Open
Abstract
Integrator (INT) is a transcriptional regulatory complex associated with RNA polymerase II that is required for the 3′-end processing of both UsnRNAs and enhancer RNAs. Integrator subunits 9 (INTS9) and INTS11 constitute the catalytic core of INT and are paralogues of the cleavage and polyadenylation specificity factors CPSF100 and CPSF73. While CPSF73/100 are known to associate with a third protein called Symplekin, there is no paralog of Symplekin within INT raising the question of how INTS9/11 associate with the other INT subunits. Here, we have identified that INTS4 is a specific and conserved interaction partner of INTS9/11 that does not interact with either subunit individually. Although INTS4 has no significant homology with Symplekin, it possesses N-terminal HEAT repeats similar to Symplekin but also contains a β-sheet rich C-terminal region, both of which are important to bind INTS9/11. We assess three functions of INT including UsnRNA 3′-end processing, maintenance of Cajal body structural integrity, and formation of histone locus bodies to conclude that INTS4/9/11 are the most critical of the INT subunits for UsnRNA biogenesis. Altogether, these results indicate that INTS4/9/11 compose a heterotrimeric complex that likely represents the Integrator ‘cleavage module’ responsible for its endonucleolytic activity.
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Affiliation(s)
- Todd R Albrecht
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Sergey P Shevtsov
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, IL 60064, USA
| | - Yixuan Wu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Lauren G Mascibroda
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Natoya J Peart
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Kai-Lieh Huang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
| | - Iain A Sawyer
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, IL 60064, USA.,Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Miroslav Dundr
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, IL 60064, USA
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77550, USA
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43
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Pu X, Meng C, Wang W, Yang S, Chen Y, Xie Q, Yu B, Liu Y. DSP1 and DSP4 Act Synergistically in Small Nuclear RNA 3' End Maturation and Pollen Growth. PLANT PHYSIOLOGY 2019; 180:2142-2151. [PMID: 31227618 PMCID: PMC6670113 DOI: 10.1104/pp.19.00231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/11/2019] [Indexed: 06/09/2023]
Abstract
Small nuclear RNAs (snRNAs) play essential roles in spliceosome assembly and splicing. Most snRNAs are transcribed by the DNA-dependent RNA polymerase II (Pol II) and require 3'-end endonucleolytic cleavage. We have previously shown that the Arabidopsis (Arabidopsis thaliana) Defective in snRNA Processing 1 (DSP1) complex, composed of at least five subunits, is responsible for snRNA 3' maturation and is essential for plant development. Yet it remains unclear how DSP1 complex subunits act together to process snRNAs. Here, we show that DSP4, a member of the metallo-β-lactamase family, physically interacts with DSP1 through its β-Casp domain. Null dsp4-1 mutants have pleiotropic developmental defects, including impaired pollen development and reduced pre-snRNA transcription and 3' maturation, resembling the phenotype of the dsp1-1 mutant. Interestingly, dsp1-1 dsp4-1 double mutants exhibit complete male sterility and reduced pre-snRNA transcription and 3'-end maturation, unlike dsp1-1 or dsp4-1 In addition, Pol II occupancy at snRNA loci is lower in dsp1-1 dsp4-1 than in either single mutant. We also detected miscleaved pre-snRNAs in dsp1-1 dsp4-1, but not in dsp1-1 or dsp4-1 Taken together, these data reveal that DSP1 and DSP4 function is essential for pollen development, and that the two cooperatively promote pre-snRNA transcription and 3'-end processing efficiency and accuracy.
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Affiliation(s)
- Xuepiao Pu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Chunmei Meng
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Weili Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Siyu Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Yuan Chen
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service and Department of Plant and Microbial Biology, University of California, Berkeley, California 94710
| | - Qingjun Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Bin Yu
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0660
| | - Yunfeng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
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44
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Skrajna A, Yang XC, Dadlez M, Marzluff WF, Dominski Z. Protein composition of catalytically active U7-dependent processing complexes assembled on histone pre-mRNA containing biotin and a photo-cleavable linker. Nucleic Acids Res 2019. [PMID: 29529248 PMCID: PMC5961079 DOI: 10.1093/nar/gky133] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
3′ end cleavage of metazoan replication-dependent histone pre-mRNAs requires the multi-subunit holo-U7 snRNP and the stem–loop binding protein (SLBP). The exact composition of the U7 snRNP and details of SLBP function in processing remain unclear. To identify components of the U7 snRNP in an unbiased manner, we developed a novel approach for purifying processing complexes from Drosophila and mouse nuclear extracts. In this method, catalytically active processing complexes are assembled in vitro on a cleavage-resistant histone pre-mRNA containing biotin and a photo-sensitive linker, and eluted from streptavidin beads by UV irradiation for direct analysis by mass spectrometry. In the purified processing complexes, Drosophila and mouse U7 snRNP have a remarkably similar composition, always being associated with CPSF73, CPSF100, symplekin and CstF64. Many other proteins previously implicated in the U7-dependent processing are not present. Drosophila U7 snRNP bound to histone pre-mRNA in the absence of SLBP contains the same subset of polyadenylation factors but is catalytically inactive and addition of recombinant SLBP is sufficient to trigger cleavage. This result suggests that Drosophila SLBP promotes a structural rearrangement of the processing complex, resulting in juxtaposition of the CPSF73 endonuclease with the cleavage site in the pre-mRNA substrate.
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Affiliation(s)
- Aleksandra Skrajna
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Xiao-Cui Yang
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michal Dadlez
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - William F Marzluff
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zbigniew Dominski
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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45
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Pettinati I, Grzechnik P, Ribeiro de Almeida C, Brem J, McDonough MA, Dhir S, Proudfoot NJ, Schofield CJ. Biosynthesis of histone messenger RNA employs a specific 3' end endonuclease. eLife 2018; 7:e39865. [PMID: 30507380 PMCID: PMC6303110 DOI: 10.7554/elife.39865] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/30/2018] [Indexed: 12/12/2022] Open
Abstract
Replication-dependent (RD) core histone mRNA produced during S-phase is the only known metazoan protein-coding mRNA presenting a 3' stem-loop instead of the otherwise universal polyA tail. A metallo β-lactamase (MBL) fold enzyme, cleavage and polyadenylation specificity factor 73 (CPSF73), is proposed to be the sole endonuclease responsible for 3' end processing of both mRNA classes. We report cellular, genetic, biochemical, substrate selectivity, and crystallographic studies providing evidence that an additional endoribonuclease, MBL domain containing protein 1 (MBLAC1), is selective for 3' processing of RD histone pre-mRNA during the S-phase of the cell cycle. Depletion of MBLAC1 in cells significantly affects cell cycle progression thus identifying MBLAC1 as a new type of S-phase-specific cancer target.
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Affiliation(s)
| | - Pawel Grzechnik
- School of BiosciencesUniversity of BirminghamBirminghamUnited Kingdom
| | | | - Jurgen Brem
- Department of ChemistryUniversity of OxfordOxfordUnited Kingdom
| | | | - Somdutta Dhir
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUnited Kingdom
| | - Nick J Proudfoot
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUnited Kingdom
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46
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Mendiratta S, Gatto A, Almouzni G. Histone supply: Multitiered regulation ensures chromatin dynamics throughout the cell cycle. J Cell Biol 2018; 218:39-54. [PMID: 30257851 PMCID: PMC6314538 DOI: 10.1083/jcb.201807179] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
Mendiratta et al. review the interplay between the different regulatory layers that affect the transcription and dynamics of distinct histone H3 variants along the cell cycle. As the building blocks of chromatin, histones are central to establish and maintain particular chromatin states associated with given cell fates. Importantly, histones exist as distinct variants whose expression and incorporation into chromatin are tightly regulated during the cell cycle. During S phase, specialized replicative histone variants ensure the bulk of the chromatinization of the duplicating genome. Other non-replicative histone variants deposited throughout the cell cycle at specific loci use pathways uncoupled from DNA synthesis. Here, we review the particular dynamics of expression, cellular transit, assembly, and disassembly of replicative and non-replicative forms of the histone H3. Beyond the role of histone variants in chromatin dynamics, we review our current knowledge concerning their distinct regulation to control their expression at different levels including transcription, posttranscriptional processing, and protein stability. In light of this unique regulation, we highlight situations where perturbations in histone balance may lead to cellular dysfunction and pathologies.
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Affiliation(s)
- Shweta Mendiratta
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Alberto Gatto
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Genevieve Almouzni
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France .,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
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47
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Targeting the Polyadenylation Signal of Pre-mRNA: A New Gene Silencing Approach for Facioscapulohumeral Dystrophy. Int J Mol Sci 2018; 19:ijms19051347. [PMID: 29751519 PMCID: PMC5983732 DOI: 10.3390/ijms19051347] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/27/2018] [Accepted: 04/30/2018] [Indexed: 02/07/2023] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is characterized by the contraction of the D4Z4 array located in the sub-telomeric region of the chromosome 4, leading to the aberrant expression of the DUX4 transcription factor and the mis-regulation of hundreds of genes. Several therapeutic strategies have been proposed among which the possibility to target the polyadenylation signal to silence the causative gene of the disease. Indeed, defects in mRNA polyadenylation leads to an alteration of the transcription termination, a disruption of mRNA transport from the nucleus to the cytoplasm decreasing the mRNA stability and translation efficiency. This review discusses the polyadenylation mechanisms, why alternative polyadenylation impacts gene expression, and how targeting polyadenylation signal may be a potential therapeutic approach for FSHD.
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48
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Grozdanov PN, Li J, Yu P, Yan W, MacDonald CC. Cstf2t Regulates expression of histones and histone-like proteins in male germ cells. Andrology 2018; 6:605-615. [PMID: 29673127 DOI: 10.1111/andr.12488] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/02/2018] [Accepted: 03/05/2018] [Indexed: 12/18/2022]
Abstract
Formation of the 3' ends of mature mRNAs requires recognition of the correct site within the last exon, cleavage of the nascent pre-mRNA, and, for most mRNAs, addition of a poly(A) tail. Several factors are involved in recognition of the correct 3'-end site. The cleavage stimulation factor (CstF) has three subunits, CstF-50 (gene symbol Cstf1), CstF-64 (Cstf2), and CstF-77 (Cstf3). Of these, CstF-64 is the RNA-binding subunit that interacts with the pre-mRNA downstream of the cleavage site. In male germ cells where CstF-64 is not expressed, a paralog, τCstF-64 (gene symbol Cstf2t) assumes its functions. Accordingly, Cstf2t knockout (Cstf2t-/- ) mice exhibit male infertility due to defective development of spermatocytes and spermatids. To discover differentially expressed genes responsive to τCstF-64, we performed RNA-Seq in seminiferous tubules from wild-type and Cstf2t-/- mice, and found that several histone and histone-like mRNAs were reduced in Cstf2t-/- mice. We further observed delayed accumulation of the testis-specific histone, H1fnt (formerly, H1t2 or Hanp1) in Cstf2t-/- mice. High-throughput sequence analysis of polyadenylation sites (A-seq) indicated reduced use of polyadenylation sites within a cluster downstream of H1fnt in knockout mice. However, high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP) was not consistent with a direct role of τCstF-64 in polyadenylation of H1fnt. These findings together suggest that the τCstF-64 may control other reproductive functions that are not directly linked to the formation of 3' ends of mature polyadenylated mRNAs during male germ cell formation.
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Affiliation(s)
- P N Grozdanov
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - J Li
- Department of Electrical and Computer Engineering & TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, USA
| | - P Yu
- Department of Electrical and Computer Engineering & TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, USA
| | - W Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - C C MacDonald
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA
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Coll O, Guitart T, Villalba A, Papin C, Simonelig M, Gebauer F. Dicer-2 promotes mRNA activation through cytoplasmic polyadenylation. RNA (NEW YORK, N.Y.) 2018; 24:529-539. [PMID: 29317541 PMCID: PMC5855953 DOI: 10.1261/rna.065417.117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 01/04/2018] [Indexed: 06/07/2023]
Abstract
Cytoplasmic polyadenylation is a widespread mechanism to regulate mRNA translation. In vertebrates, this process requires two sequence elements in target 3' UTRs: the U-rich cytoplasmic polyadenylation element and the AAUAAA hexanucleotide. In Drosophila melanogaster, cytoplasmic polyadenylation of Toll mRNA occurs independently of these canonical elements and requires a machinery that remains to be characterized. Here we identify Dicer-2 as a component of this machinery. Dicer-2, a factor previously involved in RNA interference (RNAi), interacts with the cytoplasmic poly(A) polymerase Wispy. Depletion of Dicer-2 from polyadenylation-competent embryo extracts and analysis of wispy mutants indicate that both factors are necessary for polyadenylation and translation of Toll mRNA. We further identify r2d2 mRNA, encoding a Dicer-2 partner in RNAi, as a Dicer-2 polyadenylation target. Our results uncover a novel function of Dicer-2 in activation of mRNA translation through cytoplasmic polyadenylation.
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Affiliation(s)
- Olga Coll
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003-Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003-Barcelona, Spain
| | - Tanit Guitart
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003-Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003-Barcelona, Spain
| | - Ana Villalba
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003-Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003-Barcelona, Spain
| | - Catherine Papin
- Institute of Human Genetics, CNRS UMR9002-University of Montpellier, mRNA Regulation and Development, 34396-Montpellier, France
| | - Martine Simonelig
- Institute of Human Genetics, CNRS UMR9002-University of Montpellier, mRNA Regulation and Development, 34396-Montpellier, France
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003-Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003-Barcelona, Spain
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50
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Saldi T, Fong N, Bentley DL. Transcription elongation rate affects nascent histone pre-mRNA folding and 3' end processing. Genes Dev 2018; 32:297-308. [PMID: 29483154 PMCID: PMC5859970 DOI: 10.1101/gad.310896.117] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 01/23/2018] [Indexed: 12/20/2022]
Abstract
In this study, Saldi et al. investigated how transcription elongation rate influences cotranscriptional pre-mRNA maturation. Their findings show that regulation of transcription speed can modulate pre-mRNA processing by changing nascent RNA structure and suggest a mechanism by which alternative processing could be controlled. Transcription elongation rate influences cotranscriptional pre-mRNA maturation, but how such kinetic coupling works is poorly understood. The formation of nonadenylated histone mRNA 3′ ends requires recognition of an RNA structure by stem–loop-binding protein (SLBP). We report that slow transcription by mutant RNA polymerase II (Pol II) caused accumulation of polyadenylated histone mRNAs that extend past the stem–loop processing site. UV irradiation, which decelerates Pol II elongation, also induced long poly(A)+ histone transcripts. Inhibition of 3′ processing by slow Pol II correlates with failure to recruit SLBP to histone genes. Chemical probing of nascent RNA structure showed that the stem–loop fails to fold in transcripts made by slow Pol II, thereby explaining the absence of SLBP and failure to process 3′ ends. These results show that regulation of transcription speed can modulate pre-mRNA processing by changing nascent RNA structure and suggest a mechanism by which alternative processing could be controlled.
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Affiliation(s)
- Tassa Saldi
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Nova Fong
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - David L Bentley
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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